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1,009 results for “clonal”
Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms.
<p>Datasets companion of the manuscript entitled GenAPoPop 1.0: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms, used to achieve consistency test with Spagedi 1.5 software, and used as reference datasets to demonstrate the new possibilities allowed by GenAPoPop software.</p> <p>Raw datasets used for testing GenAPoPop 1.0, A user-friendly software for easily compute genetic analyses of autopolyploid populations packaged for Linux, MacOS and Windows; Results obtained from Spagedi 1.5 (Hardy & Vekemans 2001) and GenAPoPop1.0.</p> <p>Four pseudo-observed genotyping autotetrapolyploid SNP datasets, corresponding respectively to panmictic (A), highly clonal (B), highly selfed (C) and half-clonal-half-selfed (D) reproductive mode scenario. In all these four scenarios, we simulated two populations of 100 individuals each, connected with a migration rate of 0.01 and mutating at a rate of 0.01, genotyped at 10 SNPs. Datasets were recorded 1000 generations after an initial randomly drawing population with equal allele frequencies.</p> <p>One SNP tetraploid genotyping dataset from two French <em>Ludwigia grandiflora subsp. hexapetala</em> populations (aquatic plant from the Angiosperm clade): two populations in which we collected 75 individuals, each genotyped with 36 SNPs using the Hiplex method allowing confident allele dosage (Delord et al. 2018).</p> <p>One microsatellite tetraploid genotyping dataset on two Aulactinia stella populations (sea-anemone from the Cnidaria phylum), sampled on the coast of the arctic ocean. One population of 21 individuals and one population of 15 individuals, both genotyped with 10 microsatellites.</p> <p>We also report here the consistency tests with GenAlex and Spagedi, results of analyses (GPP tab) on 6300 independant simulations and inferences of the quantitative reproductive modes using the bayesian method on CEMP tab made on 6300 another independant simulations.</p>
Data from: Reverse plasticity underlies rapid evolution by clonal selection within populations of fibroblasts propagated on a novel soft substrate
<p>Mechanical properties such as substrate stiffness are a ubiquitous feature of a cell's environment. Many types of animal cells exhibit canonical phenotypic plasticity when grown on substrates of differing stiffness, in vitro and in vivo. Whether such plasticity is a multivariate optimum due to hundreds of millions of years of animal evolution, or instead is a compromise between conflicting selective demands, is unknown. We addressed these questions by means of experimental evolution of populations of mouse fibroblasts propagated for approximately 90 cell generations on soft or stiff substrates. The ancestral cells grow twice as fast on stiff substrate as on soft substrate and exhibit the canonical phenotypic plasticity. Soft-selected lines derived from a genetically diverse ancestral population increased growth rate on soft substrate to the ancestral level on stiff substrate and evolved the same multivariate phenotype. The pattern of plasticity in the soft-selected lines was opposite of the ancestral pattern, suggesting that reverse plasticity underlies the observed rapid evolution. Conversely, growth rate and phenotypes did not change in selected lines derived from clonal cells. Overall, our results suggest that the changes were the result of genetic evolution and not phenotypic plasticity per se. Whole-transcriptome analysis revealed consistent differentiation between ancestral and soft-selected populations, and that both emergent phenotypes and gene expression tended to revert in the soft-selected lines. However, the selected populations appear to have achieved the same phenotypic outcome by means of at least two distinct transcriptional architectures related to mechanotransduction and proliferation.</p>
A Study to Investigate the Efficacy, Safety, and Tolerability of DFV890 and MAS825 for Inflammatory Marker Reduction in Adult Participants With Coronary Heart Disease and Clonal Hematopoiesis of Indet
ClinicalTrials.gov study NCT06097663. IPD Sharing: YES. Countries: 3. Publications: 1.
The emergence and development of behavioral individuality in clonal fish
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Molecular signatures of resource competition: Clonal interference favors ecological diversification and can lead to incipient speciation
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Data for: Caloric restriction extends lifespan in a clonal plant
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Aberrant basal cell clonal dynamics shape early lung carcinogenesis
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Unraveling the clonal trait space: Beyond aboveground and fine-root traits
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Data from: Inter-clonal competition over queen succession imposes a cost of parthenogenesis on termite colonies
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Variation in the location and timing of experimental severing demonstrates that the persistent rhizome serves multiple functions in a clonal forest understory herb
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Exploring the genetic consequences of clonality in haplodiplontic taxa
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Data from: Reverse plasticity underlies rapid evolution by clonal selection within populations of fibroblasts propagated on a novel soft substrate
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A generalized numerical model for clonal growth in scleractinian coral colonies
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Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity
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Individual high-quality reads (dd-RADsequencing) from: Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii
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Simulation code for: Clones on the run - the genomics of a recently expanded partially clonal species
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Data from: Caloric restriction-mediated reproductive lifespan extension across multiple strains of the clonal aquatic plant <em>Lemna turionifera</em>
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Meningococcal core and accessory phasomes vary by clonal complex
<p><em>Neisseria meningitidis </em>are Gram-negative human commensal-pathogens, with extensive phenotypic plasticity afforded by phase variable gene expression. Phase variation is a stochastic switch in gene expression from an ON to an OFF state, mediated by localised hypermutation of simple sequence repeats. Circulating <em>N. meningitidis </em>clones vary in propensity to cause disease with some clonal complexes classified as hypervirulent and others as carriage-associated. We examined the phase-variable gene repertoires, or phasome, of these lineages in order to determine if phase variation contributes to disease propensity. We analysed 3,328 genomes representative of nine circulating meningococcal clonal complexes with Phasome<em>It</em>, a tool which identifies phase-variable genes by the presence of simple sequence repeats (SSR) and homologous gene clusters. Presence, absence and functions of all identified phase-variable gene clusters were confirmed by annotation or BLAST searches within the Neisseria pubMLST database. While no significant differences were detected in the number of phase-variable genes or the core, conserved phasome content between hypervirulent and carriage lineages, individual clonal complexes exhibited major variations in phase-variable gene numbers. Phylogenetic clusters produced by phasome or core genome analyses were similar indicating co-evolution of phase-variable genes with the core genome. While conservation of phase-variable clusters is high, with 76% present in all meningococcal isolates, maintenance of an SSR is variable ranging from conserved in all isolates to present only in single clonal complexes, indicating differing evolutionary trajectories for each lineage. Diverse functional groups of PV genes were present across the meningococcal lineages, however, the majority directly or indirectly influence bacterial surface antigens and could impact on future vaccine development. Finally, we observe that meningococci have open pan phasomes, indicating on-going evolution of PV gene content and a significant potential for adaptive changes in this clinically relevant genus.</p>
Dataset used for "Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data"
<p>Each simulated dataset was generated using the AbSim R package (version 0.2.6) in a B cell single-lineage fashion. Each B cell clone simulation begins with a random selection from sets of IGHV, IGHD, and IGHJ germline sequences to produce a unique V(D)J recombination event. Then, clones are made by introducing mutations using a local nucleotide context-dependent model (S5F model) along a phylogenetic tree in which branching events occur stochastically. </p>
Data from: Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha
<p>The rhizome is a plant organ that develops from a shoot apical meristem but penetrates into belowground environments. To characterize the gene expression profile of rhizomes, we compared the rhizome transcriptome with those of the leaves, shoots and roots of a rhizomatous Brassicaceae plant, <i>Cardamine leucantha.</i> Overall, rhizome transcriptomes were characterized by the absence of genes that show rhizome-specific expression and expression profiles intermediate between those of shoots and roots. Our results suggest that both endogenous developmental factors and external environmental factors are important for controlling the rhizome transcriptome. Genes that showed relatively high expression in the rhizome compared to shoots and roots included those related to belowground defense, control of reactive oxygen species, and cell elongation under dark conditions. A comparison of transcriptomes further allowed us to identify the presence of an ER body, a defense-related belowground organelle, in epidermal cells of the <i>C. leucantha </i>rhizome, which is the first report of ER bodies in rhizome tissue.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.